{"id":"https://openalex.org/W4377965857","doi":"https://doi.org/10.1093/nar/gkad445","title":"<scp>GePI</scp> : large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions","display_name":"<scp>GePI</scp> : large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions","publication_year":2023,"publication_date":"2023-05-24","ids":{"openalex":"https://openalex.org/W4377965857","doi":"https://doi.org/10.1093/nar/gkad445","pmid":"https://pubmed.ncbi.nlm.nih.gov/37224532"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkad445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad445","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad445/50435158/gkad445.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad445/50435158/gkad445.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050377745","display_name":"Erik Faessler","orcid":"https://orcid.org/0000-0003-1193-5103"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erik Faessler","raw_affiliation_strings":["Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044841280","display_name":"Udo Hahn","orcid":"https://orcid.org/0000-0002-5052-0245"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Udo Hahn","raw_affiliation_strings":["Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016773854","display_name":"Sascha Sch\u00e4uble","orcid":null},"institutions":[{"id":"https://openalex.org/I4210162077","display_name":"Leibniz-Institut f\u00fcr Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Kn\u00f6ll-Institut (HKI)","ror":"https://ror.org/055s37c97","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210162077"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Sascha Sch\u00e4uble","raw_affiliation_strings":["Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany","Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI) , 07745 Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI) , 07745 Jena, Germany","institution_ids":["https://openalex.org/I4210162077"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5016773854"],"corresponding_institution_ids":["https://openalex.org/I4210162077","https://openalex.org/I76198965"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.9136,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.74807902,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"51","issue":"W1","first_page":"W237","last_page":"W242"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9779000282287598,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6424160003662109},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.627453088760376},{"id":"https://openalex.org/keywords/full-text-search","display_name":"Full text search","score":0.5284096002578735},{"id":"https://openalex.org/keywords/interaction-information","display_name":"Interaction information","score":0.4778989553451538},{"id":"https://openalex.org/keywords/snippet","display_name":"Snippet","score":0.46582314372062683},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.4548628032207489},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.38862642645835876},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.38591107726097107}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6424160003662109},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.627453088760376},{"id":"https://openalex.org/C20228898","wikidata":"https://www.wikidata.org/wiki/Q83540","display_name":"Full text search","level":3,"score":0.5284096002578735},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.4778989553451538},{"id":"https://openalex.org/C2777822670","wikidata":"https://www.wikidata.org/wiki/Q1120538","display_name":"Snippet","level":2,"score":0.46582314372062683},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.4548628032207489},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.38862642645835876},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.38591107726097107},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkad445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad445","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad445/50435158/gkad445.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:37224532","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37224532","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10320155","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10320155","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10320155/pdf/gkad445.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkad445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad445","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad445/50435158/gkad445.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.7900000214576721}],"awards":[{"id":"https://openalex.org/G59827103","display_name":null,"funder_award_id":"01ZZ1803G","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7052350518","display_name":null,"funder_award_id":"01ZX1402","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8287961583","display_name":null,"funder_award_id":"e:Med","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320307762","display_name":"International Business Machines Corporation","ror":"https://ror.org/05hh8d621"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320334763","display_name":"Leibniz-Gemeinschaft","ror":"https://ror.org/01n6r0e97"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4377965857.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1610821757","https://openalex.org/W2031966872","https://openalex.org/W2041187413","https://openalex.org/W2043764521","https://openalex.org/W2052947212","https://openalex.org/W2096525273","https://openalex.org/W2096951189","https://openalex.org/W2101265630","https://openalex.org/W2103017472","https://openalex.org/W2105924489","https://openalex.org/W2122863289","https://openalex.org/W2123439964","https://openalex.org/W2127224553","https://openalex.org/W2145506897","https://openalex.org/W2147154106","https://openalex.org/W2550846703","https://openalex.org/W2626179297","https://openalex.org/W2771692618","https://openalex.org/W2927760310","https://openalex.org/W2946690328","https://openalex.org/W3013678667","https://openalex.org/W3027597566","https://openalex.org/W3036559261","https://openalex.org/W3049896770","https://openalex.org/W3093053585","https://openalex.org/W3107527779","https://openalex.org/W4205440119","https://openalex.org/W4210979106","https://openalex.org/W4289274885","https://openalex.org/W4306353191","https://openalex.org/W4308834893","https://openalex.org/W4309506674","https://openalex.org/W4318263795","https://openalex.org/W6620122155","https://openalex.org/W6691630651","https://openalex.org/W6724847271","https://openalex.org/W6732090206"],"related_works":["https://openalex.org/W1484298060","https://openalex.org/W3169572532","https://openalex.org/W2111281114","https://openalex.org/W2117880470","https://openalex.org/W1716487511","https://openalex.org/W2086727654","https://openalex.org/W88942606","https://openalex.org/W2463743592","https://openalex.org/W2359796251","https://openalex.org/W2116908113"],"abstract_inverted_index":{"We":[0],"present":[1],"GePI,":[2],"a":[3,89,112,154],"novel":[4],"Web":[5,168],"server":[6],"for":[7,69],"large-scale":[8],"text":[9,155],"mining":[10],"of":[11,44,58,108,111,144,176],"molecular":[12,139],"interactions":[13,31,45,70,146],"from":[14,157],"the":[15,67,92,109,130,138,141,145,151,158],"scientific":[16],"biomedical":[17],"literature.":[18],"GePI":[19,40,191],"leverages":[20],"natural":[21],"language":[22],"processing":[23],"techniques":[24],"to":[25,51,71,96,129],"identify":[26],"genes":[27,57],"and":[28,35,118,153,173,178,188],"related":[29],"entities,":[30,140],"between":[32],"those":[33],"entities":[34],"biomolecular":[36],"events":[37],"involving":[38],"them.":[39],"supports":[41],"rapid":[42],"retrieval":[43],"based":[46],"on":[47],"powerful":[48],"search":[49,68],"options":[50],"contextualize":[52],"queries":[53],"targeting":[54],"(lists":[55],"of)":[56],"interest.":[59],"Contextualization":[60],"is":[61,85,192],"enabled":[62],"by":[63,150],"full-text":[64],"filters":[65],"constraining":[66],"either":[72],"sentences":[73],"or":[74,77],"paragraphs,":[75],"with":[76,114,135,184],"without":[78],"pre-defined":[79],"gene":[80,177],"lists.":[81],"Our":[82],"knowledge":[83],"graph":[84],"updated":[86],"several":[87],"times":[88],"week":[90],"ensuring":[91],"most":[93],"recent":[94],"information":[95,136],"be":[97],"available":[98,193],"at":[99,194],"all":[100],"times.":[101],"The":[102],"result":[103],"page":[104],"provides":[105],"an":[106],"overview":[107],"outcome":[110],"search,":[113],"accompanying":[115],"interaction":[116,132,180],"statistics":[117],"visualizations.":[119],"A":[120],"table":[121],"(downloadable":[122],"in":[123,182],"Excel":[124],"format)":[125],"gives":[126],"direct":[127],"access":[128],"retrieved":[131],"pairs,":[133],"together":[134],"about":[137],"factual":[142],"certainty":[143],"(as":[147],"verbatim":[148],"expressed":[149],"authors),":[152],"snippet":[156],"original":[159],"document":[160],"that":[161],"verbalizes":[162],"each":[163],"interaction.":[164],"In":[165],"summary,":[166],"our":[167],"application":[169],"offers":[170],"free,":[171],"easy-to-use,":[172],"up-to-date":[174],"monitoring":[175],"protein":[179],"information,":[181],"company":[183],"flexible":[185],"query":[186],"formulation":[187],"filtering":[189],"options.":[190],"https://gepi.coling.uni-jena.de/.":[195]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2023-05-25T00:00:00"}
